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Simulating Linkage Disequilibrium Structures in a Human Population for SNP Association Studies

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Abstract

Existing simulation methods usually simulate linkage disequilibrium (LD) structures starting with an initial population that is randomly generated according to specified allele frequencies. These at random based methods might be unstable because the LD level of the initial population is generally extremely low. This study presents a new algorithm, SIMLD, to simulate genome populations with real LD structures. SIMLD begins from an initial population with possibly the highest LD level, and then the LD decays to fit the desired level through processes of mating and recombination over generations. SIMLD can produce case–control samples according to various disease models. Using empirical SNP marker information from three populations of HapMap data, we implement the proposed algorithm and demonstrate a set of experimental results.

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Acknowledgments

This work was supported in part by the National Science Fund of China under Grant nos. 61070137, 60933009, and 60371044, and by the U.S. National Institutes of Health under Grants GM085665, HL090567, and NS029525.

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Authors and Affiliations

  1. School of Computer Science and Technology, Xidian University, Xi’an, 710071, China

    Xiguo Yuan & Junying Zhang

  2. Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, 22203, USA

    Xiguo Yuan & Yue Wang

Authors
  1. Xiguo Yuan
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  2. Junying Zhang
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  3. Yue Wang
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Correspondence to Xiguo Yuan.

Electronic supplementary material

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10528_2011_9416_MOESM1_ESM.doc

Simulated LD for sim500SNPs_data. D′ values by distance are given in the comparisons between the simulated data and real populations, JPT/CHB (a), CEU (b), and YRI (c) (DOC 41 kb)

10528_2011_9416_MOESM2_ESM.doc

Simulated LD for sim1000SNPs_data. D′ values by distance are given in the comparisons of simulated data and real data for populations (a) JPT/CHB, (b) CEU, and (c) YRI (DOC 42 kb)

10528_2011_9416_MOESM3_ESM.doc

Simulated LD for sim2000SNPs_data. D′ values by distance are given in the comparisons of simulated data and real data for populations (a) JPT/CHB, (b) CEU, and (c) YRI (DOC 41 kb)

10528_2011_9416_MOESM4_ESM.doc

Simulated LD for sim5000SNPs_data. D′ values by distance are given in the comparisons of simulated data and real data for populations (a) JPT/CHB, (b) CEU, and (c) YRI (DOC 41 kb)

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Yuan, X., Zhang, J. & Wang, Y. Simulating Linkage Disequilibrium Structures in a Human Population for SNP Association Studies. Biochem Genet 49, 395–409 (2011). https://doi.org/10.1007/s10528-011-9416-x

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  • DOI: https://doi.org/10.1007/s10528-011-9416-x

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